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Accession IconSRP102178

A high temperature RNA-seq dataset for studies of gene expression variation in the MAGIC line resource of Arabidopsis thaliana

Organism Icon Arabidopsis thaliana
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Technology Badge IconIllumina HiSeq 2000

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To understand expression phenotypes in Arabidopsis thaliana at high temperature, a set of the Multiparent Advanced Generation Inter-Cross (MAGIC) recombinant inbred lines were grown under long day conditions (16 hours light: 8 hours dark) at 20°C and then shifted to 30°C for 48 hours. RNA was collected at the 4th true leaf stage, and RNA-seq data was generated using the Illumina method. The MAGIC lines included are largely a subset of lines for which comparable RNA-seq data was collected at a constant 20°C (allowing the same genotypes to be compared at 20°C and after the high temperature shift at approximately the same developmental stage and under otherwise the same growth conditions). The read data for the analogous low temperature study can be found under GEO submission GSE94107. Overall design: In total 103 RNA-seq samples from different inbred lines from the Multiparent Advance Generation InterCross (MAGIC) population in the reference plant, Arabidopsis thaliana, were generated. For each sample, RNA was collected from the aerial shoot from 20 seedlings at the 4th true leaf stage (after a temperature shift from 20°C to 30°C), and Illumina mRNA-seq libraries were constructed (a single library was constructed with each line; that is, each MAGIC line is represented by one biological replicate). Using these libraries, which were non-stranded, paired-end 100 bp RNA-seq Illumina reads were generated for each sample, and used to quantify gene expresison in each MAGIC line. The resulting expression phenotypes are suitable for describing the impacts of segregating genetic variation on the control of gene expression.
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